4YBB

High-resolution structure of the Escherichia coli ribosome

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, V (AA, BA)	16S rRNA	polymer	1534	497405.0	2	GenBank (731469900)	Escherichia coli K-12
2	B, W (AB, BB)	30S ribosomal protein S2	polymer	224	24971.8	2	UniProt (P0A7V0) Pfam (PF00318)	Escherichia coli (strain K12)
3	C, X (AC, BC)	30S ribosomal protein S3	polymer	206	23078.8	2	UniProt (P0A7V3) Pfam (PF07650) Pfam (PF00189)	Escherichia coli (strain K12)
4	D, Y (AD, BD)	30S ribosomal protein S4	polymer	205	23383.0	2	UniProt (P0A7V8) Pfam (PF00163) Pfam (PF01479)	Escherichia coli (strain K12)
5	E, Z (AE, BE)	30S ribosomal protein S5	polymer	155	16361.9	2	UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719)	Escherichia coli (strain K12)
6	AA, F (AF, BF)	30S ribosomal protein S6	polymer	106	12326.3	2	UniProt (P02358) Pfam (PF01250)	Escherichia coli (strain K12)
7	BA, G (AG, BG)	30S ribosomal protein S7	polymer	151	16861.5	2	UniProt (P02359) Pfam (PF00177)	Escherichia coli (strain K12)
8	CA, H (AH, BH)	30S ribosomal protein S8	polymer	129	14015.4	2	UniProt (P0A7W7) Pfam (PF00410)	Escherichia coli (strain K12)
9	DA, I (AI, BI)	30S ribosomal protein S9	polymer	127	14554.9	2	UniProt (P0A7X3) Pfam (PF00380)	Escherichia coli (strain K12)
10	EA, J (AJ, BJ)	30S ribosomal protein S10	polymer	99	11325.1	2	UniProt (P0A7R5) Pfam (PF00338)	Escherichia coli (strain K12)
11	FA, K (AK, BK)	30S ribosomal protein S11	polymer	117	12487.2	2	UniProt (P0A7R9) Pfam (PF00411)	Escherichia coli (strain K12)
12	GA, L (AL, BL)	30S ribosomal protein S12	polymer	123	13683.1	2	UniProt (P0A7S3) Pfam (PF00164)	Escherichia coli (strain K12)
13	HA, M (AM, BM)	30S ribosomal protein S13	polymer	114	12625.8	2	UniProt (P0A7S9) Pfam (PF00416)	Escherichia coli (strain K12)
14	IA, N (AN, BN)	30S ribosomal protein S14	polymer	100	11475.4	2	UniProt (P0AG59) Pfam (PF00253)	Escherichia coli (strain K12)
15	JA, O (AO, BO)	30S ribosomal protein S15	polymer	88	10159.6	2	UniProt (P0ADZ4) Pfam (PF00312)	Escherichia coli (strain K12)
16	KA, P (AP, BP)	30S ribosomal protein S16	polymer	82	9207.6	2	UniProt (P0A7T3) Pfam (PF00886)	Escherichia coli (strain K12)
17	LA, Q (AQ, BQ)	30S ribosomal protein S17	polymer	80	9263.9	2	UniProt (P0AG63) Pfam (PF00366)	Escherichia coli (strain K12)
18	MA, R (AR, BR)	30S ribosomal protein S18	polymer	55	6466.5	2	UniProt (P0A7T7) Pfam (PF01084)	Escherichia coli (strain K12)
19	NA, S (AS, BS)	30S ribosomal protein S19	polymer	79	9057.6	2	UniProt (P0A7U3) Pfam (PF00203)	Escherichia coli (strain K12)
20	OA, T (AT, BT)	30S ribosomal protein S20	polymer	86	9577.3	2	UniProt (P0A7U7) Pfam (PF01649)	Escherichia coli (strain K12)
21	PA, U (AU, BU)	30S ribosomal protein S21	polymer	56	6629.7	2	UniProt (P68679) Pfam (PF01165)	Escherichia coli (strain K12)
22	QA (CA)	23S rRNA	polymer	2904	941809.6	1	GenBank (731469900)	Escherichia coli K-12
23	RA, WB (CB, DB)	5S rRNA	polymer	120	38790.1	2	GenBank (731469900)	Escherichia coli K-12
24	SA, XB (CC, DC)	50S ribosomal protein L2	polymer	271	29663.2	2	UniProt (P60422) Pfam (PF00181) Pfam (PF03947)	Escherichia coli (strain K12)
25	TA (CD)	50S ribosomal protein L3	polymer	209	22277.5	1	UniProt (P60438) Pfam (PF00297)	Escherichia coli (strain K12)
26	UA, ZB (CE, DE)	50S ribosomal protein L4	polymer	201	22121.6	2	UniProt (P60723) Pfam (PF00573)	Escherichia coli (strain K12)
27	AC, VA (CF, DF)	50S ribosomal protein L5	polymer	177	20073.2	2	UniProt (P62399) Pfam (PF00281) Pfam (PF00673)	Escherichia coli (strain K12)
28	BC, WA (CG, DG)	50S ribosomal protein L6	polymer	176	18801.6	2	UniProt (P0AG55) Pfam (PF00347)	Escherichia coli (strain K12)
29	CC, XA (CH, DH)	50S ribosomal protein L9	polymer	149	15789.0	2	UniProt (P0A7R1) Pfam (PF01281) Pfam (PF03948)	Escherichia coli (strain K12)
30	EC, YA (CJ, DJ)	50S ribosomal protein L11	polymer	134	14020.3	2	UniProt (P0A7J7) Pfam (PF03946) Pfam (PF00298)	Escherichia coli (strain K12)
31	FC, ZA (CK, DK)	50S ribosomal protein L13	polymer	142	16050.6	2	UniProt (P0AA10) Pfam (PF00572)	Escherichia coli (strain K12)
32	AB, GC (CL, DL)	50S ribosomal protein L14	polymer	123	13565.1	2	UniProt (P0ADY3) Pfam (PF00238)	Escherichia coli (strain K12)
33	BB, HC (CM, DM)	50S ribosomal protein L15	polymer	144	15008.5	2	UniProt (P02413) Pfam (PF00828)	Escherichia coli (strain K12)
34	CB, IC (CN, DN)	50S ribosomal protein L16	polymer	136	15327.3	2	UniProt (P0ADY7) Pfam (PF00252)	Escherichia coli (strain K12)
35	DB, JC (CO, DO)	50S ribosomal protein L17	polymer	125	14193.5	2	UniProt (P0AG44) Pfam (PF01196)	Escherichia coli (strain K12)
36	EB, KC (CP, DP)	50S ribosomal protein L18	polymer	117	12794.7	2	UniProt (P0C018) Pfam (PF00861)	Escherichia coli (strain K12)
37	FB, LC (CQ, DQ)	50S ribosomal protein L19	polymer	114	13028.1	2	UniProt (P0A7K6) Pfam (PF01245)	Escherichia coli (strain K12)
38	GB, MC (CR, DR)	50S ribosomal protein L20	polymer	117	13396.8	2	UniProt (P0A7L3) Pfam (PF00453)	Escherichia coli (strain K12)
39	HB, NC (CS, DS)	50S ribosomal protein L21	polymer	103	11586.4	2	UniProt (P0AG48) Pfam (PF00829)	Escherichia coli (strain K12)
40	IB, OC (CT, DT)	50S ribosomal protein L22	polymer	110	12253.4	2	UniProt (P61175) Pfam (PF00237)	Escherichia coli (strain K12)
41	JB, PC (CU, DU)	50S ribosomal protein L23	polymer	93	10546.5	2	UniProt (P0ADZ0) Pfam (PF00276)	Escherichia coli (strain K12)
42	KB, QC (CV, DV)	50S ribosomal protein L24	polymer	102	11078.9	2	UniProt (P60624) Pfam (PF00467) Pfam (PF17136)	Escherichia coli (strain K12)
43	LB, RC (CW, DW)	50S ribosomal protein L25	polymer	94	10713.5	2	UniProt (P68919) Pfam (PF01386)	Escherichia coli (strain K12)
44	MB, SC (CX, DX)	50S ribosomal protein L27	polymer	76	8275.5	2	UniProt (P0A7L8) Pfam (PF01016)	Escherichia coli (strain K12)
45	NB, TC (CY, DY)	50S ribosomal protein L28	polymer	77	8896.4	2	UniProt (P0A7M2) Pfam (PF00830)	Escherichia coli (strain K12)
46	OB, UC (CZ, DZ)	50S ribosomal protein L29	polymer	62	7155.3	2	UniProt (P0A7M6) Pfam (PF00831)	Escherichia coli (strain K12)
47	PB, VC (C0, D0)	50S ribosomal protein L30	polymer	58	6423.6	2	UniProt (P0AG51) Pfam (PF00327)	Escherichia coli (strain K12)
48	QB, WC (C1, D1)	50S ribosomal protein L32	polymer	56	6332.2	2	UniProt (P0A7N4) Pfam (PF01783)	Escherichia coli (strain K12)
49	RB, XC (C2, D2)	50S ribosomal protein L33	polymer	51	5928.0	2	UniProt (P0A7N9) Pfam (PF00471)	Escherichia coli
50	SB, YC (C3, D3)	50S ribosomal protein L34	polymer	46	5397.5	2	UniProt (P0A7P5) Pfam (PF00468)	Escherichia coli (strain K12)
51	TB, ZC (C4, D4)	50S ribosomal protein L35	polymer	64	7181.8	2	UniProt (P0A7Q1) Pfam (PF01632)	Escherichia coli (strain K12)	Ribosomal protein A
52	AD, UB (C5, D5)	50S ribosomal protein L36	polymer	38	4377.4	2	UniProt (P0A7Q6) Pfam (PF00444)	Escherichia coli (strain K12)	Ribosomal protein B
53	VB (DA)	23S rRNA	polymer	2903	941505.4	1	GenBank (731469900)	Escherichia coli K-12
54	YB (DD)	50S ribosomal protein L3	polymer	209	22291.6	1	UniProt (P60438) Pfam (PF00297)	Escherichia coli (strain K12)
55	DC (DI)	50S ribosomal protein L10	polymer	135	14568.7	1	UniProt (P0A7J3) Pfam (PF00466)	Escherichia coli (strain K12)	50S ribosomal protein L8
56	AE, AF, AH, AI, AJ... (AA, BA, CA, DA, DR...)	MAGNESIUM ION	non-polymer		24.3	463	Chemie (MG)
57	EW, GV, LX, NX, QX... (DA, DQ, DR, DS, BA...)	TETRAETHYLENE GLYCOL	non-polymer		194.2	7	Chemie (PG4)
58	DV, DX, EX, FV, FX... (DA, DE, DK, DN, DS...)	(4S)-2-METHYL-2,4-PENTANEDIOL	non-polymer		118.2	14	Chemie (MPD)
59	AW, BV, BW, CV, HW... (DA, DM, AA)	1,4-DIAMINOBUTANE	non-polymer		88.2	16	Chemie (PUT)
60	AG, AY, VN (AB, D5, C5)	ZINC ION	non-polymer		65.4	3	Chemie (ZN)
61	BG, GW, GX, JX, KX... (AL, DA, DL, DP, DQ...)	DI(HYDROXYETHYL)ETHER	non-polymer		106.1	11	Chemie (PEG)
62	AV, MW, UV, WU (DA)	SPERMIDINE	non-polymer		145.2	4	Chemie (SPD)
63	QV, YU (DA)	PENTAETHYLENE GLYCOL	non-polymer		238.3	2	Chemie (1PE)
64	CW, FW, NW, PX, RV... (DA, DS, DU, D1, D3)	TRIETHYLENE GLYCOL	non-polymer		150.2	9	Chemie (PGE)
65	EV, JV, PV (DA)	ACETIC ACID	non-polymer		60.1	3	Chemie (ACY)
66	AX, BX, CX, DW, HV... (DB, DA, DR, D0, D1)	1,2-ETHANEDIOL	non-polymer		62.1	12	Chemie (EDO)
67	ZV (DA)	GUANINE	non-polymer		151.1	1	Chemie (GUN)
68	IW (DA)	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL	non-polymer		122.1	1	Chemie (TRS)
69	AAA, AZ, BAA, BY, BZ... (DK, BT, DL, AA, BU...)	water	water		18.0	7750	Chemie (HOH)

Sequence modifications

CA: 1 - 2904 (GenBank: 731469900)

PDB	External Database	Details
U 2798	Unk 4143004	conflict
A 2800	Unk 4143006	conflict

DA: 1 - 2903 (GenBank: 731469900)

PDB	External Database	Details
U 2798	Unk 4143004	conflict
A 2800	Unk 4143006	conflict

DI: 2 - 136 (UniProt: P0A7J3)

PDB	External Database	Details
Val 85	Ser 85	conflict
Thr 86	Met 86	conflict

Contents of the asymmetric unit

Polymers	Number of chains	105
	Total formula weight	4249826.5
Non-Polymers*	Number of molecules	546
	Total formula weight	20648.5
All*	Total formula weight	4270475.1

*Water molecules are not included.